#!/usr/bin/env python
"""main Absorb routines
Copyright: 2009, Robert B. Von Dreele (Argonne National Laboratory)
"""
from __future__ import division, print_function
import platform
import math
import sys
import wx
# the next line removes the need for pythonw. Thanks to Matt Newville!
# appears unneaded from wx 4.2.1 on
if sys.platform.lower() == 'darwin': wx.PyApp.IsDisplayAvailable = lambda _: True
import numpy as np
import sys
import matplotlib as mpl
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5743 $")
import GSASIIElem as G2elem
import GSASIIElemGUI as G2elemGUI
import GSASIIctrlGUI as G2G
try:
wx.NewIdRef
wx.NewId = wx.NewIdRef
except AttributeError:
pass
if '2' in platform.python_version_tuple()[0]:
Gktheta = unichr(0x3b8)
Gklambda = unichr(0x3bb)
GkDelta = unichr(0x0394)
Pwr10 = unichr(0x0b9)+unichr(0x2070)
Pwr20 = unichr(0x0b2)+unichr(0x2070)
Pwrm1 = unichr(0x207b)+unichr(0x0b9)
Pwrm2 = unichr(0x207b)+unichr(0x0b2)
Pwrm6 = unichr(0x207b)+unichr(0x2076)
Pwrm4 = unichr(0x207b)+unichr(0x2074)
Angstr = unichr(0x00c5)
Gkmu = unichr(0x3bc)
Pwr3 = unichr(0x0b3)
Pwr4 = unichr(0x2074)
Pwr20 = unichr(0x0b2)+unichr(0x0b0)
Pwrm1 = unichr(0x207b)+unichr(0x0b9)
else:
Gktheta = chr(0x3b8)
Gklambda = chr(0x3bb)
GkDelta = chr(0x0394)
Pwr10 = chr(0x0b9)+chr(0x2070)
Pwr20 = chr(0x0b2)+chr(0x2070)
Pwrm1 = chr(0x207b)+chr(0x0b9)
Pwrm2 = chr(0x207b)+chr(0x0b2)
Pwrm6 = chr(0x207b)+chr(0x2076)
Pwrm4 = chr(0x207b)+chr(0x2074)
Angstr = chr(0x00c5)
Gkmu = chr(0x3bc)
Pwr3 = chr(0x0b3)
Pwr4 = chr(0x2074)
Pwr20 = chr(0x0b2)+chr(0x0b0)
Pwrm1 = chr(0x207b)+chr(0x0b9)
[wxID_CHOICE1, wxID_SPINTEXT1, wxID_SPINTEXT2, wxID_SPINTEXT3, wxID_SPINTEXT4,
wxID_RESULTS,wxID_SLIDER1, wxID_SPINBUTTON, wxID_NUMELEM, wxID_SPINTEXT5,wxID_SPINTEXT6,
] = [wx.NewId() for _init_ctrls in range(11)]
[wxID_EXIT, wxID_DELETE, wxID_NEW,
] = [wx.NewId() for _init_coll_ABSORB_Items in range(3)]
[wxID_KALPHAAGKA, wxID_KALPHACOKA, wxID_KALPHACRKA,
wxID_KALPHACUKA, wxID_KALPHAFEKA, wxID_KALPHAMNKA,
wxID_KALPHAMOKA, wxID_KALPHANIKA, wxID_KALPHAZNKA,
wxID_KALPHAGAKA,wxID_KALPHAINKA,
] = [wx.NewId() for _init_coll_KALPHA_Items in range(11)]
[wxID_ABSORBABOUT] = [wx.NewId() for _init_coll_ABOUT_Items in range(1)]
[docs]
class Absorb(wx.Frame):
'''Creates a frame where input for absorption calculation is supplied
'''
Elems = []
Wave = 1.5405 #CuKa default
Kev = 12.397639 #keV for 1A x-rays
for arg in sys.argv:
if '-w' in arg:
Wave = float(arg.split('-w')[1])
elif '-e' in arg:
E = float(arg.split('-e')[1])
Wave = Kev/E
elif '-h' in arg:
print ('''
Absorb.py can take the following arguments:
-h - this help listing
-wv - set default wavelength to v, e.g. -w1.54 sets wavelength to 1.54A
-ev - set default energy to v, e.g. -e27 sets energy to 27keV
without arguments Absorb uses CuKa as default (Wave=1.54052A, E=8.0478keV)
''')
sys.exit()
Wmin = 0.05 #wavelength range
Wmax = 3.0
Wres = 0.004094 #plot resolution step size as const delta-lam/lam - gives 1000 steps for Wmin to Wmax
Eres = 1.5e-4 #typical energy resolution for synchrotron x-ray sources
Energy = Kev/Wave
ifWave = True
Volume = 0
ifVol = False
Zcell = 1
Pack = 0.50
Radius = 0.4
def _init_coll_ABOUT_Items(self, parent):
parent.Append(wxID_ABSORBABOUT,'About')
self.Bind(wx.EVT_MENU, self.OnABOUTItems0Menu, id=wxID_ABSORBABOUT)
def _init_coll_menuBar1_Menus(self, parent):
parent.Append(menu=self.ABSORB, title='Absorb')
parent.Append(menu=self.KALPHA, title='Kalpha')
parent.Append(menu=self.ABOUT, title='About')
def _init_coll_KALPHA_Items(self, parent):
"Set of characteristic radiation from sealed tube sources"
def OnCrkaMenu(event):
self.SetWaveEnergy(2.28962)
def OnMnkaMenu(event):
self.SetWaveEnergy(2.10174)
def OnFekaMenu(event):
self.SetWaveEnergy(1.93597)
def OnCokaMenu(event):
self.SetWaveEnergy(1.78896)
def OnNikaMenu(event):
self.SetWaveEnergy(1.65784)
def OnCukaMenu(event):
self.SetWaveEnergy(1.54052)
def OnZnkaMenu(event):
self.SetWaveEnergy(1.43510)
def OnGakaMenu(event):
self.SetWaveEnergy(1.34134)
def OnMokaMenu(event):
self.SetWaveEnergy(0.70926)
def OnAgkaMenu(event):
self.SetWaveEnergy(0.55936)
def OnInkaMenu(event):
self.SetWaveEnergy(0.51357)
parent.Append(wxID_KALPHACRKA, 'CrKa')
parent.Append(wxID_KALPHAMNKA, 'MnKa')
parent.Append(wxID_KALPHAFEKA, 'FeKa')
parent.Append(wxID_KALPHACOKA, 'CoKa')
parent.Append(wxID_KALPHANIKA, 'NiKa')
parent.Append(wxID_KALPHACUKA, 'CuKa')
parent.Append(wxID_KALPHAZNKA, 'ZnKa')
parent.Append(wxID_KALPHAGAKA, 'GaKa')
parent.Append(wxID_KALPHAMOKA, 'MoKa')
parent.Append(wxID_KALPHAAGKA, 'AgKa')
parent.Append(wxID_KALPHAINKA, 'InKa')
self.Bind(wx.EVT_MENU, OnCrkaMenu, id=wxID_KALPHACRKA)
self.Bind(wx.EVT_MENU, OnMnkaMenu, id=wxID_KALPHAMNKA)
self.Bind(wx.EVT_MENU, OnFekaMenu, id=wxID_KALPHAFEKA)
self.Bind(wx.EVT_MENU, OnCokaMenu, id=wxID_KALPHACOKA)
self.Bind(wx.EVT_MENU, OnNikaMenu, id=wxID_KALPHANIKA)
self.Bind(wx.EVT_MENU, OnCukaMenu, id=wxID_KALPHACUKA)
self.Bind(wx.EVT_MENU, OnZnkaMenu, id=wxID_KALPHAZNKA)
self.Bind(wx.EVT_MENU, OnGakaMenu, id=wxID_KALPHAGAKA)
self.Bind(wx.EVT_MENU, OnMokaMenu, id=wxID_KALPHAMOKA)
self.Bind(wx.EVT_MENU, OnAgkaMenu, id=wxID_KALPHAAGKA)
self.Bind(wx.EVT_MENU, OnInkaMenu, id=wxID_KALPHAINKA)
def _init_coll_ABSORB_Items(self, parent):
parent.Append(wxID_NEW,'&New Element','Add new element')
self.Delete = parent.Append(wxID_DELETE,'&Delete Element','Delete an element')
self.Delete.Enable(False)
parent.Append(wxID_EXIT,'&Exit','Exit Fprime')
self.Bind(wx.EVT_MENU, self.OnExitMenu, id=wxID_EXIT)
self.Bind(wx.EVT_MENU, self.OnNewMenu, id=wxID_NEW)
self.Bind(wx.EVT_MENU, self.OnDeleteMenu, id=wxID_DELETE)
def _init_utils(self):
self.ABSORB = wx.Menu(title='')
self.KALPHA = wx.Menu(title='')
self.KALPHA.SetEvtHandlerEnabled(True)
self.ABOUT = wx.Menu(title='')
self.menuBar1 = wx.MenuBar()
self._init_coll_ABSORB_Items(self.ABSORB)
self._init_coll_KALPHA_Items(self.KALPHA)
self._init_coll_ABOUT_Items(self.ABOUT)
self._init_coll_menuBar1_Menus(self.menuBar1)
def _init_ctrls(self, parent):
wx.Frame.__init__(self, parent=parent,
size=wx.Size(500, 400),style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX, title='Absorb')
self._init_utils()
self.SetMenuBar(self.menuBar1)
self.DrawPanel()
[docs]
def SetSize(self):
w,h = self.GetClientSize()
self.panel.SetSize(wx.Size(w,h))
def DrawPanel(self):
self.panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
self.Results = wx.TextCtrl( parent=self.panel,
style=wx.TE_MULTILINE|wx.TE_DONTWRAP )
self.Results.SetEditable(False)
mainSizer.Add(self.Results,1,wx.EXPAND)
mainSizer.Add((10,15),0)
if self.Elems:
lablSizer = wx.BoxSizer(wx.HORIZONTAL)
lablSizer.Add((5,10),0)
lablSizer.Add(wx.StaticText(parent=self.panel,label='Chemical Formula:'),0,
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_LEFT)
mainSizer.Add(lablSizer,0)
mainSizer.Add((5,5),0)
nRow = len(self.Elems)//5
compSizer = wx.FlexGridSizer(nRow+1,10,0,0)
for Elem in self.Elems:
compSizer.Add(wx.StaticText(parent=self.panel,label=" "+Elem[0].capitalize(),
size=wx.Size(30,20)),0,wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
numElem = wx.TextCtrl(id=wxID_NUMELEM,parent=self.panel,name=Elem[0],
size=wx.Size(70,20),value="%.2f" % (Elem[2]),style=wx.TE_PROCESS_ENTER)
compSizer.Add(numElem,0)
numElem.Bind(wx.EVT_TEXT_ENTER, self.OnNumElem, id=wxID_NUMELEM)
mainSizer.Add(compSizer,0)
mainSizer.Add((10,15),0)
selSizer = wx.BoxSizer(wx.HORIZONTAL)
selSizer.Add((5,10),0)
selSizer.Add(wx.StaticText(parent=self.panel, label='Wavelength:'),0,wx.EXPAND)
selSizer.Add((5,10),0)
self.SpinText1 = wx.TextCtrl(id=wxID_SPINTEXT1, parent=self.panel,
size=wx.Size(100,20), value = "%.4f" % (self.Wave),style=wx.TE_PROCESS_ENTER )
selSizer.Add(self.SpinText1,0)
selSizer.Add((5,10),0)
self.SpinText1.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText1, id=wxID_SPINTEXT1)
selSizer.Add(wx.StaticText(parent=self.panel, label='Energy:'),0,wx.EXPAND)
selSizer.Add((5,10),0)
self.SpinText2 = wx.TextCtrl(id=wxID_SPINTEXT2, parent=self.panel,
size=wx.Size(100,20), value = "%.4f" % (self.Energy),style=wx.TE_PROCESS_ENTER)
selSizer.Add(self.SpinText2,0)
selSizer.Add((5,10),0)
self.SpinText2.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText2, id=wxID_SPINTEXT2)
selSizer.Add(wx.StaticText(parent=self.panel, label='Plot scale:'),0,wx.EXPAND)
selSizer.Add((5,10),0)
self.choice1 = wx.ComboBox(id=wxID_CHOICE1, parent=self.panel, value='Wavelength',
choices=['Wavelength','Energy'],style=wx.CB_READONLY|wx.CB_DROPDOWN)
selSizer.Add(self.choice1,0)
selSizer.Add((10,10),0)
self.choice1.Bind(wx.EVT_COMBOBOX, self.OnChoice1, id=wxID_CHOICE1)
mainSizer.Add(selSizer,0)
mainSizer.Add((10,10),0)
slideSizer = wx.BoxSizer(wx.HORIZONTAL)
self.SpinButton = wx.SpinButton(id=wxID_SPINBUTTON, parent=self.panel,
size=wx.Size(25,24), style=wx.SP_VERTICAL | wx.SP_ARROW_KEYS)
slideSizer.Add(self.SpinButton)
self.SpinButton.SetRange(-1,1)
self.SpinButton.SetValue(0)
self.SpinButton.Bind(wx.EVT_SPIN, self.OnSpinButton, id=wxID_SPINBUTTON)
self.slider1 = G2G.G2Slider(id=wxID_SLIDER1, maxValue=int(1000.*self.Wmax),
minValue=int(1000.*self.Wmin), parent=self.panel,style=wx.SL_HORIZONTAL,
value=int(self.Wave*1000.), )
slideSizer.Add(self.slider1,1,wx.EXPAND)
self.slider1.Bind(wx.EVT_SLIDER, self.OnSlider1, id=wxID_SLIDER1)
mainSizer.Add(slideSizer,0,wx.EXPAND)
mainSizer.Add((10,10),0)
cellSizer = wx.BoxSizer(wx.HORIZONTAL)
cellSizer.Add((5,10),0)
cellSizer.Add(wx.StaticText(parent=self.panel, label='Volume:'),0,wx.EXPAND)
cellSizer.Add((5,10),0)
self.SpinText3 = wx.TextCtrl(id=wxID_SPINTEXT3, parent=self.panel,
size=wx.Size(100,20), value = "%.2f" % (self.Volume),style=wx.TE_PROCESS_ENTER )
cellSizer.Add(self.SpinText3,0)
cellSizer.Add((5,10),0)
self.SpinText3.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText3, id=wxID_SPINTEXT3)
cellSizer.Add((5,10),0)
cellSizer.Add(wx.StaticText(parent=self.panel, label='Z(vol):'),0,wx.EXPAND)
cellSizer.Add((5,10),0)
self.SpinText4 = wx.TextCtrl(id=wxID_SPINTEXT4, parent=self.panel,
size=wx.Size(50,20), value = "%d" % (self.Zcell),style=wx.TE_PROCESS_ENTER )
cellSizer.Add(self.SpinText4,0)
cellSizer.Add((5,10),0)
self.SpinText4.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText4, id=wxID_SPINTEXT4)
cellSizer.Add((5,10),0)
cellSizer.Add(wx.StaticText(parent=self.panel, label='Sample R:'),0,wx.EXPAND)
cellSizer.Add((5,10),0)
self.SpinText5 = wx.TextCtrl(id=wxID_SPINTEXT5, parent=self.panel,
size=wx.Size(50,20), value = "%.2f" % (self.Radius),style=wx.TE_PROCESS_ENTER )
cellSizer.Add(self.SpinText5,0)
cellSizer.Add((5,10),0)
self.SpinText5.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText5, id=wxID_SPINTEXT5)
cellSizer.Add((5,10),0)
cellSizer.Add(wx.StaticText(parent=self.panel, label='packing:'),0,wx.EXPAND)
cellSizer.Add((5,10),0)
self.SpinText6 = wx.TextCtrl(id=wxID_SPINTEXT6, parent=self.panel,
size=wx.Size(50,20), value = "%.2f" % (self.Pack),style=wx.TE_PROCESS_ENTER )
cellSizer.Add(self.SpinText6,0)
cellSizer.Add((5,10),0)
self.SpinText6.Bind(wx.EVT_TEXT_ENTER, self.OnSpinText6, id=wxID_SPINTEXT6)
mainSizer.Add(cellSizer,0)
mainSizer.Add((10,10),0)
self.panel.SetSizer(mainSizer)
self.panel.Fit()
self.panel.GetParent().SetSize()
def __init__(self, parent):
self._init_ctrls(parent)
self.parent = parent
self.Lines = []
self.Elems = []
self.linePicked = None
def OnExitMenu(self, event):
self.parent.G2plotNB.Delete('Absorb')
self.Close()
self.Destroy()
def OnNewMenu(self, event):
ElList = []
for Elem in self.Elems: ElList.append(Elem[0])
PE = G2elemGUI.PickElements(self,ElList)
if PE.ShowModal() == wx.ID_OK:
Elem = PE.Elem
PE.Destroy()
if Elem:
for El in Elem:
ElemSym = El.strip().upper()
if ElemSym not in ElList:
atomData = G2elem.GetAtomInfo(ElemSym.capitalize())
FormFactors = G2elem.GetFormFactorCoeff(ElemSym)
for FormFac in FormFactors:
FormSym = FormFac['Symbol'].strip()
if FormSym == ElemSym:
Z = FormFac['Z'] #At. No.
N = 1. #no atoms / formula unit
Orbs = G2elem.GetXsectionCoeff(ElemSym)
Elem = [ElemSym,Z,N,FormFac,Orbs,atomData]
self.Elems.append(Elem)
self.ifVol = False
self.Delete.Enable(True)
self.panel.Destroy()
self.DrawPanel()
self.NewFPPlot = True
self.SetWaveEnergy(self.Wave)
def OnDeleteMenu(self, event):
if len(self.Elems):
ElList = []
for Elem in self.Elems: ElList.append(Elem[0])
S = []
DE = G2elemGUI.DeleteElement(self,ElList)
if DE.ShowModal() == wx.ID_OK:
El = DE.GetDeleteElement().strip().upper()
for Elem in self.Elems:
if Elem[0] != El:
S.append(Elem)
self.Elems = S
self.CalcFPPS()
if not self.Elems:
self.Delete.Enable(False)
self.panel.Destroy()
self.DrawPanel()
self.ifVol = False
self.NewFPPlot = True
self.SetWaveEnergy(self.Wave)
def OnNumElem(self, event):
for Elem in self.Elems:
if event.GetEventObject().GetName() == Elem[0]:
Elem[2] = float(event.GetEventObject().GetValue())
event.GetEventObject().SetValue("%8.2f" % (Elem[2]))
self.ifVol = False
self.SetWaveEnergy(self.Wave)
def OnSpinText1(self, event):
self.SetWaveEnergy(float(self.SpinText1.GetValue()))
def OnSpinText2(self, event):
self.SetWaveEnergy(self.Kev/(float(self.SpinText2.GetValue())))
def OnSpinText3(self,event):
self.Volume = max(10.,float(self.SpinText3.GetValue()))
self.ifVol = True
self.SetWaveEnergy(self.Wave)
def OnSpinText4(self,event):
self.Zcell = max(1,float(self.SpinText4.GetValue()))
self.SetWaveEnergy(self.Wave)
def OnSpinText5(self, event):
self.Radius = max(0.01,float(self.SpinText5.GetValue()))
self.SetWaveEnergy(self.Wave)
def OnSpinText6(self, event):
self.Pack = min(1.0,max(0.01,float(self.SpinText6.GetValue())))
self.SetWaveEnergy(self.Wave)
def OnSpinButton(self, event):
move = self.SpinButton.GetValue()/10000.
self.Wave = min(max(self.Wave+move,self.Wmin),self.Wmax)
self.SpinButton.SetValue(0)
self.SetWaveEnergy(self.Wave)
def OnSlider1(self, event):
if self.ifWave:
Wave = float(self.slider1.GetValue())/1000.
else:
Wave = self.Kev/(float(self.slider1.GetValue())/1000.)
self.SetWaveEnergy(Wave)
def SetWaveEnergy(self,Wave):
self.Wave = Wave
self.Energy = self.Kev/self.Wave
self.Energy = round(self.Energy,4)
E = self.Energy
DE = E*self.Eres #smear by defined source resolution
self.SpinText1.SetValue("%.4f" % (self.Wave))
self.SpinText2.SetValue("%.4f" % (self.Energy))
self.SpinText1.Update()
self.SpinText2.Update()
if self.ifWave:
self.slider1.SetValue(int(1000.*self.Wave))
else:
self.slider1.SetValue(int(1000.*self.Energy))
Text = ''
if not self.ifVol:
self.Volume = 0
for Elem in self.Elems:
self.Volume += 10.*Elem[2]
muT = 0
Mass = 0
Fo = 0
Fop = 0
for Elem in self.Elems:
Mass += self.Zcell*Elem[2]*Elem[5]['Mass']
r1 = G2elem.FPcalc(Elem[4],E+DE)
r2 = G2elem.FPcalc(Elem[4],E-DE)
Els = Elem[0]
Els = Els.ljust(2).lower().capitalize()
mu = 0
Fo += Elem[2]*Elem[1]
if Elem[1] > 78 and self.Energy+DE > self.Kev/0.16:
mu = self.Zcell*Elem[2]*(r1[2]+r2[2])/2.0
Text += "%s\t%s%8.2f %s%6s %s%6.3f %s%10.2f %s\n" % (
'Element: '+str(Els),"N = ",Elem[2]," f'=",'not valid',
' f"=',(r1[1]+r2[1])/2.0,' '+Gkmu+'=',mu,'barns')
elif Elem[1] > 94 and self.Energy-DE < self.Kev/2.67:
mu = 0
Text += "%s\t%s%8.2f %s%6s %s%6s %s%10s%s\n" % (
'Element: '+str(Els),"N = ",Elem[2]," f'=",'not valid',
' f"=','not valid',' '+Gkmu+'=',mu,'not valid')
else:
mu = self.Zcell*Elem[2]*(r1[2]+r2[2])/2.0
Fop += Elem[2]*(Elem[1]+(r1[0]+r2[0])/2.0)
Text += "%s\t%s%8.2f %s%6.3f %s%6.3f %s%10.2f %s\n" % (
'Element: '+str(Els),"N = ",Elem[2]," f'=",(r1[0]+r2[0])/2.0,
' f"=',(r1[1]+r2[1])/2.0,' '+Gkmu+'=',mu,'barns')
muT += mu
if self.Volume:
Text += "%s %s%10.4g %s" % ("Total",' '+Gkmu+' =',self.Pack*muT/self.Volume,'cm'+Pwrm1+', ')
Text += "%s%10.4g%s" % ('Total '+Gkmu+'R =',self.Radius*self.Pack*muT/(10.0*self.Volume),', ')
Text += "%s%10.4f%s\n" % ('Transmission exp(-2'+Gkmu+'R) =', \
100.0*math.exp(-2.*self.Radius*self.Pack*muT/(10.0*self.Volume)),'%')
if muT > 0.:
pene = 10./(self.Pack*muT/self.Volume)
if pene > 0.01:
Text += "%s %10.4g mm\n"%("1/e (~27.2%) penetration depth = ",pene)
else:
Text += "%s %10.4g %sm\n"%("1/e (~27.2%) penetration depth = ",1000.0*pene,Gkmu)
self.Results.SetValue(Text)
den = Mass/(0.602*self.Volume)
if self.ifVol:
Text += '%s' % ('Theor. density =')
else:
Text += '%s' % ('Est. density =')
Text += '%6.3f %s%.3f %s\n' % (den,'g/cm'+Pwr3+', Powder density =',self.Pack*den,'g/cm'+Pwr3)
Text += '%s%10.2f%s\n'%('X-ray small angle scattering contrast',(28.179*Fo/self.Volume)**2,'*10'+Pwr20+'/cm'+Pwr4)
if Fop:
Text += '%s%10.2f%s\n'%('Anomalous X-ray small angle scattering contrast',(28.179*Fop/self.Volume)**2,'*10'+Pwr20+'/cm'+Pwr4)
self.Results.SetValue(Text)
self.Results.Update()
self.SpinText3.SetValue("%.2f" % (self.Volume))
self.SpinText3.Update()
self.SpinText4.SetValue("%d" % (self.Zcell))
self.SpinText4.Update()
self.SpinText5.SetValue("%.2f" % (self.Radius))
self.SpinText5.Update()
self.SpinText6.SetValue("%.2f" % (self.Pack))
self.SpinText6.Update()
if len(self.Elems):
self.CalcFPPS()
self.UpDateAbsPlot(Wave,rePlot=True)
[docs]
def CalcFPPS(self):
"""generate f" curves for selected elements
does constant delta-lambda/lambda steps over defined range
"""
FPPS = []
if self.Elems:
wx.BeginBusyCursor()
Corr = self.Zcell*self.Radius*self.Pack/(10.0*self.Volume)
try:
muT = []
for iE,Elem in enumerate(self.Elems):
Els = Elem[0]
Els = Els = Els.ljust(2).lower().capitalize()
Wmin = self.Wmin
Wmax = self.Wmax
lWmin = math.log(Wmin)
N = int(round(math.log(Wmax/Wmin)/self.Wres)) #number of constant delta-lam/lam steps
I = range(N+1)
Ws = []
for i in I: Ws.append(math.exp(i*self.Wres+lWmin))
mus = []
Es = []
for j,W in enumerate(Ws):
E = self.Kev/W
DE = E*self.Eres #smear by defined source resolution
res1 = G2elem.FPcalc(Elem[4],E+DE)
res2 = G2elem.FPcalc(Elem[4],E-DE)
muR = Corr*Elem[2]*(res1[2]+res2[2])/2.0
mus.append(muR)
if iE:
muT[j] += muR
else:
muT.append(muR)
Es.append(E)
if self.ifWave:
Fpps = (Els,Ws,mus)
else:
Fpps = (Els,Es,mus)
FPPS.append(Fpps)
if self.ifWave:
Fpps = ('Total',Ws,muT)
else:
Fpps = ('Total',Es,muT)
FPPS.append(Fpps)
finally:
wx.EndBusyCursor()
self.FPPS = FPPS
def OnChoice1(self, event):
if event.GetString() == "Wavelength":
self.ifWave = True
self.NewFPPlot = True
self.Wave = round(self.Wave,4)
self.slider1.SetRange(int(1000.*self.Wmin),int(1000.*self.Wmax))
self.slider1.SetValue(int(1000.*self.Wave))
self.SpinText1.SetValue("%6.4f" % (self.Wave))
self.SpinText2.SetValue("%7.4f" % (self.Energy))
else:
self.ifWave = False
self.NewFPPlot = True
Emin = self.Kev/self.Wmax
Emax = self.Kev/self.Wmin
self.Energy = round(self.Energy,4)
self.slider1.SetRange(int(1000.*Emin),int(1000.*Emax))
self.slider1.SetValue(int(1000.*self.Energy))
self.SpinText1.SetValue("%6.4f" % (self.Wave))
self.SpinText2.SetValue("%7.4f" % (self.Energy))
if len(self.Elems):
self.CalcFPPS()
self.UpDateAbsPlot(self.Wave,rePlot=False)
def OnKeyPress(self,event):
if event.key == 'g':
mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid']
self.UpDateAbsPlot(self.Wave,rePlot=False)
[docs]
def UpDateAbsPlot(self,Wave,rePlot=True):
"""Plot mu vs wavelength 0.05-3.0A"""
xylim = []
try:
if rePlot:
asb = self.Page.figure.get_axes()[1]
xylim = asb.get_xlim(),asb.get_ylim()
newPlot = False
except:
new,plotNum,self.Page,self.fplot,lim = self.parent.G2plotNB.FindPlotTab('Absorb','mpl')
self.Page.canvas.mpl_connect('pick_event', self.OnPick)
self.Page.canvas.mpl_connect('button_release_event', self.OnRelease)
self.Page.canvas.mpl_connect('motion_notify_event', self.OnMotion)
self.Page.canvas.mpl_connect('key_press_event', self.OnKeyPress)
newPlot = True
self.ax = self.Page.figure.add_subplot(111,label='absorb')
self.fplot.set_visible(False)
self.Page.Choice = (' key press','g: toggle grid',)
self.Page.keyPress = self.OnKeyPress
self.ax.clear()
self.ax.set_title('X-Ray Absorption',x=0,ha='left')
self.ax.set_ylabel(r"$\mu R$",fontsize=14)
Ymin = 0.0
Ymax = 0.0
if self.FPPS:
for Fpps in self.FPPS:
Ymin = min(Ymin,min(Fpps[2]))
Ymax = max(Ymax,max(Fpps[2]))
fppsP1 = np.array(Fpps[1])
fppsP2 = np.array(Fpps[2])
self.ax.plot(fppsP1,fppsP2,label=r'$\mu R$ '+Fpps[0])
if self.ifWave:
self.ax.set_xlabel(r'$\mathsf{\lambda, \AA}$',fontsize=14)
self.ax.axvline(x=Wave,picker=3,color='black')
else:
self.ax.set_xlabel(r'$\mathsf{E, keV}$',fontsize=14)
self.ax.set_xscale('log')
self.ax.axvline(x=self.Kev/Wave,picker=3,color='black')
self.ax.axhline(y=1.0,color='b')
self.ax.axhline(y=5.0,color='r')
self.ax.set_ylim(Ymin,Ymax)
if self.FPPS:
self.ax.legend(loc='best')
if newPlot:
newPlot = False
self.Page.canvas.draw()
else:
if rePlot:
tb = self.Page.canvas.toolbar
tb.push_current()
self.ax.set_xlim(xylim[0])
self.ax.set_ylim(xylim[1])
xylim = []
tb.push_current()
self.Page.canvas.draw()
def OnPick(self, event):
self.linePicked = event.artist
def OnMotion(self,event):
xpos = event.xdata
if xpos and xpos>0.1:
ypos = event.ydata
if self.ifWave:
Wave = xpos
else:
Wave = self.Kev/xpos
Wave = min(max(Wave,self.Wmin),self.Wmax)
self.parent.G2plotNB.status.SetStatusText('Wavelength: %.4f, Energy: %.3f, %sR: %.3f'%(Wave,self.Kev/Wave,Gkmu,ypos),1)
if self.linePicked:
self.SetWaveEnergy(Wave)
def OnRelease(self, event):
if self.linePicked is None: return
self.linePicked = None
xpos = event.xdata
if xpos:
if self.ifWave:
Wave = xpos
else:
Wave = self.Kev/xpos
self.SetWaveEnergy(Wave)
if __name__ == "__main__":
import GSASIIplot as G2plt
app = wx.App()
GSASIIpath.InvokeDebugOpts()
frm = wx.Frame(None) # create a frame
frm.Show(False)
size = wx.Size(700,700)
frm.plotFrame = wx.Frame(frm,-1,'GSASII Plots',size=size,
style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
frm.plotFrame.Show()
frm.G2plotNB = G2plt.G2PlotNoteBook(frm.plotFrame,G2frame=frm)
abswin = Absorb(frm)
abswin.Show()
abswin.Bind(wx.EVT_WINDOW_DESTROY,lambda event: sys.exit())
app.MainLoop()